407: Bioremediation/Wastewater/Vaccines/Biomining/Synthetic

Bioremediation

using living organisms to remove/neutralize pollutants

Ex-situ bioremediation

removing polluted material from its original location and treating it elsewhere

In-situ bioremediation

treating pollutants directly at the site

Biomineralization

living organisms turn dissolved substances into solid materials

Xenobiotics

chemical compounds that are foreign to biological system and not naturally found in environment

Pollutant

The accumulation of anything in the wrong place/balance

Inorganic pollutants

don’t contain carbon, heavy metals, lead, radionuclides (uranium)

they don’t break down easily

Organic pollutants

break down over time with carbon and hydrogen

ex. oil, hydrocarbons, pesticides

Biomineralization

turn dissolved substances into solid materials

Biofiltration

using microorganisms to filter pollutants from air/water

• Microbes in a filter breaking down volatile organic compounds in air

Bioattenuation

letting natural microbes naturally reduce pollution over time

• Contaminated groundwater slowly cleaning itself

Bioventing

adding air to soil to help microbes degrade pollutants

• pumping oxygen into contaminated soil to boost activity of aerobic microbes

Biostimulation

adding nutrients to help microbes break down pollutants

• adding nitrogen/phosphorus to contaminated soil

Bioaugmentation

adding specific microbes to help cleanup pollution

• Introduce oil-degrading bacteria to an oil spill site

Microbial groups that reduce Uranium

1. Metal-reducing: shewanella and geobacter species

2. Sulfate-reducing: desulfovibrio species

electron donor in Uranium bioremediation

acetate

uraninite in oxic environment

contact with manganese oxide, reoxidizes to soluble U6+ state

 U-238 

• Most common isotope

• equal to age of earth

• must be managed cuz super radioactive

key enzyme in degrading hydrocarbon

oxygenase: brings in oxygen to attract microbes

oil eating microbe

Alcanivorax borkumensis

• loves growing on hydrocarbons, fatty acids and pyruvate

biosurfactant

surface chemical to help break down oil

problematic hydrocarbons

branched-chain and polycyclic hydrocarbons

• complex molecular structure

microbes in VR degradation

bacillus cereus, staphylococcus aureus and rhodococcus

examples of xenobiotics

• pesticides

• polychlorinated biphenyls: air cooler

• munitions: bomb

• dyes

• chlorinated solvents

fungus that can break down plastic

fusarium

bacteria that can break down plastic

ideonella sakaiensis

fusarium breaks down PET into what

terephthalic acid

PHA’s have equal amounts of:

poly-B-hydroxybutyrate and poly-B-hydroxyvalerate

wastewater

domestic sewage/liquid industrial waste that can’t be discarded

effluent

wastewater that can be released to lakes/streams

sewage

effluent that is contaminated with human/animal fecal and has pathogens

domestic wastewater

grey water from homes: washing, bathing, cooking

industrial waste water

water from manufacturing industries

toxic substances in industrial waste water

• cyanide

• heavy metals: arsenic, lead, mercury

• organic materials: acrylamide and benzene

BOD

biochemical oxygen demand

• amount of dissolved oxygen that microbes consume to break down organic matter in a sample

sludge flocs are made of

clumps of microbes and extracellular polymeric substances (glue) EPS

secondary treatment is oxic/anoxic

oxic

key bacteria and organisms in the activated sludge

• slime forming aerobic bacteria

  • zoogloea ramigera a type of betaproteobacteria

  • protists, small animals, filamentous bacteria and fungi

tertiary treatment purpose

• remove any remaining BOD

• remove toxic materials

• remove inorganic nutrients that support microbe growth

potable water

safe to drink

turbidity

measures how cloudy/murky water is due to suspended particles

suspended soils

small solid particles that float in water

chemicals added in sedimentation

• anionic polymers

• aluminum sulfate

• chlorine

filtration

removes organic/inorganic solutes and other suspended particles

the filters have

thick layers of sand, activated charcoal, ion exchangers

what bacteria chlorine cant kill and why

cryptospordium

• has protective shell of oocysts that can survive in harsh conditions

chlorine analyse

determine level of chlorine needed to be added to maintain enough chlorine residual to stop microbes from growing

wavelength of UV

260 nm

chlorine gets added (two ways)

1. as liquid solution sodium hypochlorite or or calcium hypochlorite

2. as chlorine gas in pressurized tank

when chlorine gas dissolves in water it makes

hypochlorous acid

vaccine

substance that gives immunity to a disease when injected into an animal

attenuated vaccine

weakened, viable

delete bad genes keep ones to make an immune response

vector vaccine

carrier virus genome has genes from the pathogenic virus

it delivers it to the cell to make antigens of the pathogen

our immune system learns to recognize the antigens to develop immunity

polyvalent vaccine

• protects from many strains of single pathogen

• genes from one inserted into another

• must be compatible

subunit vaccine

contains immunogenic proteins

• not live, just the proteins

why was yeast in the hepatitis B subunit vaccine

hep B needs glycosylation by the host before if can be active

• proteins made in yeast which glycosylates and activates teh vaccine

good bacteria for cancer therapy are

anaerobic like in the intestinal tract and in tumors

Type 1 diabetes case study

in T1: the immune cells destroy cells in pancreas that make insulin

• lactobacillus delivers a GLP, glucagon like peptide in a rat model can reprogram its intestinal cells to respond to glucose and make insulin

• epithelial cells naturally shed so its temporary

Cystic Fibrosis case study

in CF Pseudomonas aeruginosa causes biofilms that make patients have lung infections

• engineer a probiotic E.coli

• recognizes P.aeruginosa via quorum sensing molecules AHL

two therapeutic molecules probiotic e.coli delivers

dispersin: breaks down the biofilms

bacteriocin: kills p.aeruginosa cells by lysing them

Listeria case study

Listeria monocytogenes is a foodborne pathogen

• engineer the weakened strains to express tumor specific antigens

• can also carry toxic drugs/radioisotopes to tumors

• immune system will produce antibodies and attack

• destroy bacteria and tumor cells

three components of anthrax toxin

PA: protective antigen - helps toxin enter cells

EF: edema factor - causes swelling

LF : lethal factor - causes cell death

anthrax case study

PA: protective antigen that helps toxin enter cells is engineered to have an antibody that binds to tumor cell

• tumor cell engulfs this PA and antibody and makes an endosome

• PA makes a pore in the membrane so the antibody can go into the cytoplasm of tumor cell

• it recruits the immune system and destroys it

pyrite

most common form of iron in nature

found in coal and metal ores

key species in microbial leaching

acidithiobacillus ferroxidans

chemolithortroph

gets energy by oxidizing inroganic compounds

easily leached ores by acidithiobacillus

iron sulfides: pyrrhotite FeS

copper sulfides: covellite CuS

hard to leach ores

lead and molybdenum

• less reactive chemical structures

temperatures and microrganisms

• mesophilic

• thermophilic

• hyperthermophilic

mesophilic: moderate temp: A. ferroxidans

thermophilic: iron-oxidizing: leptospirillum ferroxidans

hyperthermophilic: higher temps: archaea like sulfolobus predominate

what is the product of uranium leaching

UO2 to UO2SO4 which is very soluble

how is gold usually found in nature

with arsenic and FeS2 materials

how is arsenic removes in gold leaching

as ferric precipitate

what happens to cyanide in gold recovery

bacteria oxidize CN- to CO2 and later urea

synthetic biology

using biological systems to make things that wouldnt happen naturally in nature

reverse engineering

understanding how biological processes occur by reconstructing them

forward engineering

making new biological systems from scratch

biosensor

device that turns a biological response into an electrical signal (ex. insulin, covid test)

elements of biosensor

1. bioreceptor: interacts with substance being detected

2. tranducer: converts the interaction to a signal that can be measured like current, light, heat

3. electronics: used to process and amplify the signal

4. display: output that shows the final results in digital form

Arsenic in water case

• arsenic contaminates drinking water

• biosensor to detect aersenic

• uses ArsR protein that usually binds DNA and stops gene expression

• when arsenic is present, it binds ArsR and releases the DNA, turning on gene expression

• mCherry gene makes visible red fluorescence to show presence of arsenic

Golden rice case

• vitamin A deficiency in ppl that use rice

• engineer beta- caroteine in rice grain

• using agrobacterium that naturally injects a part of its plasmid in a plant to make a tumor

• this gets transformed to make a transgenic plant with beta-caroteine

enzymes the convert b-carotene in golden rice

phytoene synthase

phytoene desaturase

n-lycopene cyclase

lightbulb project

• caffeic acid cycle in fungi makes bioluminescence with enzyme luciferase

• it turns substrates into light then recycles itself and restarts cycle

• they cut restriction enzymes Type IIS to express the caffeic acid pathway and light bulb

Type IIS enzyme special

it cuts outside of its range allowing for custom overhangs